6-71647057-T-C

Variant names:

• chr6-71647057-T-C
• rs9446432
• ENST00000787970.1:n.181-39946T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000787970.1(ENSG00000302585):​n.181-39946T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,084 control chromosomes in the GnomAD database, including 1,763 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.13 (1763 hom., cov: 33)
• Consequence: ENSG00000302585 ENST00000787970.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 7 publications found

Genes affected

ENSG00000302585 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000787970.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302585	ENST00000787970.1		n.181-39946T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20386 AN: 151968 Hom.: 1750 Cov.: 33

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.0502

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.0745

Gnomad FIN AF: 0.0698

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0846

Gnomad OTH AF: 0.125

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.134 AC: 20441 AN: 152084 Hom.: 1763 Cov.: 33 AF XY: 0.134 AC XY: 9995 AN XY: 74334

African (AFR) AF: 0.207 AC: 8596 AN: 41482

American (AMR) AF: 0.228 AC: 3486 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0502 AC: 174 AN: 3468

East Asian (EAS) AF: 0.164 AC: 849 AN: 5166

South Asian (SAS) AF: 0.0740 AC: 356 AN: 4810

European-Finnish (FIN) AF: 0.0698 AC: 738 AN: 10568

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0845 AC: 5749 AN: 68002

Other (OTH) AF: 0.130 AC: 274 AN: 2110

Alfa AF: 0.0914 Hom.: 397

Bravo AF: 0.153

Asia WGS AF: 0.173 AC: 603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.68
PhyloP100		0.31

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9446432; hg19: chr6-72356760;